Bottom Line:
Taken together, our map shows the general information of nucleosome dynamics reasonably well.The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity.Furthermore, the associations with gene function and histone modification were also discussed here.

ABSTRACTAlthough nucleosome remodeling is essential to transcriptional regulation in eukaryotes, little is known about its genome-wide behavior. Since a number of nucleosome positioning maps in vivo have been recently determined, we examined if their comparisons might be used for obtaining a genome-wide profile of nucleosome remodeling. Using seven yeast maps, the local variability of nucleosomes, measured by the entropy, was significantly higher in a set of reported unstable nucleosomes. The binding sites of four transcription factors, known as the remodeling factors, were distinctively high both in entropy and linker ratio, whereas those of Yhp1, their potential inhibitor, showed the lowest values in both of them. Taken together, our map shows the general information of nucleosome dynamics reasonably well. The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity. Furthermore, the associations with gene function and histone modification were also discussed here.

Fig5: Nucleosome dynamics and gene expression. a Clusters of genes plotted by the entropy/linker ratio values. Clusters 1 to 4 are represented by black, red, green, and blue, respectively. Difference of b the expression variety and d the expression intensity among the four clusters. c A relationship between the expression variety and the entropy. Genes are classified into 20 clusters by expression variety

Mentions:
Since chromatin remodeling is involved in transcriptional regulation, it is of interest to study the correlation between our data and systematic gene expression data. First, we plotted 5,089 genes based on the entropy and the linker ratio, averaged over their upstream 400-bp region (Fig. 2). Roughly speaking, these two values correlate with each other, but there exists a group of exceptional genes that have larger linker ratios than expected. Second, we classified these 5,089 genes into four clusters by Ward's method and tried to characterize each of them (clusters 1 to 4 in Fig. 5a and Supplementary Fig. 6). Each cluster contained 1,142, 788, 1,289, and 1,870 genes, respectively (Supplementary Table 5). Since the entropy and the linker ratio in cluster 1 were the highest, this cluster was interpreted as having “dynamic and open” promoters. On the other hand, cluster 2 showed the lowest entropy and linker ratio, characterized as “stable and closed”. As noted above, cluster 3 is exceptional because it has lower entropy but higher linker ratio. This cluster of genes is expected to have “stable and open” promoters.Fig. 5

Fig5: Nucleosome dynamics and gene expression. a Clusters of genes plotted by the entropy/linker ratio values. Clusters 1 to 4 are represented by black, red, green, and blue, respectively. Difference of b the expression variety and d the expression intensity among the four clusters. c A relationship between the expression variety and the entropy. Genes are classified into 20 clusters by expression variety

Mentions:
Since chromatin remodeling is involved in transcriptional regulation, it is of interest to study the correlation between our data and systematic gene expression data. First, we plotted 5,089 genes based on the entropy and the linker ratio, averaged over their upstream 400-bp region (Fig. 2). Roughly speaking, these two values correlate with each other, but there exists a group of exceptional genes that have larger linker ratios than expected. Second, we classified these 5,089 genes into four clusters by Ward's method and tried to characterize each of them (clusters 1 to 4 in Fig. 5a and Supplementary Fig. 6). Each cluster contained 1,142, 788, 1,289, and 1,870 genes, respectively (Supplementary Table 5). Since the entropy and the linker ratio in cluster 1 were the highest, this cluster was interpreted as having “dynamic and open” promoters. On the other hand, cluster 2 showed the lowest entropy and linker ratio, characterized as “stable and closed”. As noted above, cluster 3 is exceptional because it has lower entropy but higher linker ratio. This cluster of genes is expected to have “stable and open” promoters.Fig. 5

Bottom Line:
Taken together, our map shows the general information of nucleosome dynamics reasonably well.The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity.Furthermore, the associations with gene function and histone modification were also discussed here.

ABSTRACTAlthough nucleosome remodeling is essential to transcriptional regulation in eukaryotes, little is known about its genome-wide behavior. Since a number of nucleosome positioning maps in vivo have been recently determined, we examined if their comparisons might be used for obtaining a genome-wide profile of nucleosome remodeling. Using seven yeast maps, the local variability of nucleosomes, measured by the entropy, was significantly higher in a set of reported unstable nucleosomes. The binding sites of four transcription factors, known as the remodeling factors, were distinctively high both in entropy and linker ratio, whereas those of Yhp1, their potential inhibitor, showed the lowest values in both of them. Taken together, our map shows the general information of nucleosome dynamics reasonably well. The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity. Furthermore, the associations with gene function and histone modification were also discussed here.